1. When you compile the document, you only need to typeset the Thesis_Template.tex file, the chapters won’t typeset individually as they are input with the \include command.
2. Good folder and file structure will make your life much easier.
3. Use a single bibliography file for the entire thesis, and call it at the end of the Thesis_Template.tex file.
4. When labelling chapters, sections, figures, tables, etc., make sure you don’t repeat names or the compiler will get confused.
5. Likewise, don’t put spaces into file/folder names or paths.
6. Remember to typeset multiple times when you want to refresh the contents page, or when referencing sections.